**Remark.** The condition that $\bigcup_{r \geq 0} \ker(\phi^r)(k)$ is Zariski dense is not needed. Indeed, if it is not satisfied, replace $\phi$ by $[\ell] \circ \phi$ for $\ell$ invertible in $k$. Since $([\ell] \circ \phi)^r = [\ell^r] \circ \phi^r$, the kernel contains all $\ell^r$-torsion, which is Zariski dense as $r \to \infty$.

Moreover, $[\ell] \circ \phi$ satisfies $(*)$ if $\phi$ does. Indeed, if $x \in \ker([\ell^r] \circ \phi^r)$, then
$$([\ell^r] \circ \phi^r) (\lambda(x)) = \phi^r(\lambda([\ell^r]x)) = 0,$$
since $[\ell^r]x \in \ker \phi^r$ and by condition $(*)$ for $\phi$. Thus, $\lambda(x) \in \ker([\ell^r] \circ \phi^r)$, which proves condition $(*)$ for $[\ell] \circ \phi$.

Finally, $\phi^{-1} \circ \lambda \circ \phi$ is unaffected by this replacement, since scalars are central.

**Negative answer to your question.** Let $A = E \times E$ be the square of an elliptic curve. Let $\phi \colon (x,y) \mapsto (y,x)$ be the swap isomorphism, and let $\lambda \colon (x,y) \mapsto (x,0)$ be the projection. Condition $(*)$ is now trivially satisfied (there is no kernel).

But $\phi^{-1} \circ \lambda \circ \phi$ is now the other coordinate projection $(x,y) \mapsto (0,y)$. This is not of the form $\lambda \circ c$ for any $c$, for example since the images don't agree (even after inverting scalars). Nor is it of the form $c \circ \lambda$, because the kernels don't agree.

**Is there anything we can say?** The best I can do is the following: condition $(*)$ implies, by the fundamental theorem on homomorphisms¹, that there exist maps $\lambda_r \colon A \to A$ such that the diagrams
$$\begin{array}{ccc}A & \stackrel\lambda\longrightarrow & A \\ {\tiny{\phi^r}}\downarrow\ \ & & \ \ \downarrow\tiny{\phi^r} \\ A & \stackrel{\lambda_r}\longrightarrow & A \end{array}$$
commute. In fact, this is equivalent to condition $(*)$: the converse follows from the diagram.

But as we saw above, the relation between $\lambda_1$ and $\lambda$ is not something simple like $\lambda_1 = \lambda \circ c$ or $\lambda_1 = c \circ \lambda$ for some $c$.

¹One should say some words about set-theoretic inclusion and scheme-theoretic inclusion in $(*)$. This should be fine because $\ker(\phi^r)$ is an étale $k$-scheme, and $k$ is algebraically closed.